Genus-level taxonomic changes implied by the mitochondrial phylogeny of grey mullets (Teleostei: Mugilidae)

Freshwater fishes of Israel; a revised and updated annotated checklist2023

The current status of the freshwater fishes of Israel is revised, and an updated checklist is presented. The confirmed freshwater fishes of Israel comprise 55 species belonging to nine orders, 14 families, and 39 genera. Among these, 19 species (34.6%) are alien, and four species (7.3%) are considered endemic to Israel. The orders with the largest numbers of species in the ichthyofauna of Israel are Cypriniformes (19 species), followed by Cichliformes (14 species), Cyprinodontiformes (seven species), Mugiliformes (six species), Siluriformes (four species), Salmoniformes (two species), and the others represent one species in each. At the family level, the Cichlidae have the greatest number of species (14 species; 25.5% of the total species), followed by Cyprinidae (10 species), Leuciscidae and Mugilidae (six species in each), Aphaniidae (four species), Nemacheilidae and Poecilidae (three species in each). According to IUCN Red List criteria, among 36 naturally distributed species (alien species not included), two species are extinct (EX) and nine species (25.0%) are categorized as threatened extinctions, with two (5.6%) CR, four (11.1%) EN, and three (8.3%) VU.

Freshwater fishes of Syria: a revised and updated annotated checklist-2023

The current status of the freshwater fishes of Syria is revised, and an updated checklist is presented. The confirmed freshwater fishes of Syria comprise 108 species belonging to 15 orders, 25 families, and 51 genera. Among these, 11 species (10.2%) are alien, and six species (5.6%) are considered endemic to Syria. The orders with the largest numbers of species in the ichthyofauna of Syria are Cypriniformes (68 species), followed by Siluriformes and (nine species), Cichliformes (eight species), Mugiliformes (seven species), Cyprinodontiformes (six species), and others represent one species in each. At the family level, Cyprinidae has the greatest number of species (30 species; 27.8% of the total species), followed by Leuciscidae (21 species), Nemacheilidae (11 species), Cichlidae (eight species), and Mugilidae (seven species). According to IUCN Red List criteria, among 97 naturally distributed species (alien species not included), Tristramella sacra extinct (EX) and 24 species (26.5%) are categorized as threatened extinctions, CR, EN, and VU (eight species in each). A total of 17 species previously reported from Syria have been excluded from the checklist, either in the present study or in previous studies.

Atlantor, a new generic name for Barbus reinii Günther, 1874 from Morocco(Teleostei: Cyprinidae)

Atlantor, new genus, is proposed for Barbus reinii from the Atlantic basin in Morocco. The sole species of the genus is clearly separated from related genera based on its phylogenetic position, and from Carasobarbus, Mesopotamichthys and Pterocapoeta in its morphological characters. Atlantor was previously included in Labeobarbus, making this genus paraphyletic with respect to several genera from Western Asia and North Africa. With the description of Atlantor, all these genera become monophyletic. Within Torinae, Atlantor can be diagnosed by having 5½ branched anal-fin rays, modally 8½ branched dorsal-fin rays, two pairs of long barbels, and by its distinct phylogenetic position.

Lack of genetic structure in euryhaline Chelon labrosus from the estuaries under anthropic pressure in the Southern Bay of Biscay to the coastal waters of the Mediterranean Sea

Over the last decade, xenoestrogenic effects have been reported in populations of thicklip grey mullet Chelon labrosus from contaminated estuaries in the Bay of Biscay, resulting in intersex condition. To understand the level of gene flow in individuals of different Basque estuaries microsatellite markers were used to evaluate the population structure and connectivity of C. labrosus from estuaries of the Basque coast. 46 microsatellites were tested and 10 validated for the analysis of 204 individuals collected from 5 selected Basque estuaries and 2 outgroups in the Bay of Cadiz and Thermaic Gulf. The polymorphic microsatellites revealed 74 total alleles, 2-19 alleles per locus. The mean observed heterozygosity (0.49 ± 0.02) was lower than the expected one (0.53 ± 0.01). There was no evidence of genetic differentiation (F_ST = 0.0098, P = 0.0000) among individuals or sites. Bayesian clustering analysis revealed a single population in all sampled locations. The results of this study indicate widespread genetic homogeneity and panmixia of C. labrosus across the current sampling areas spanning the Atlantic and Mediterranean basins. The hypothesis of panmixia could therefore be well supported so individuals inhabiting estuaries with high prevalence of intersex condition should be considered as members of the same single genetic group as those inhabiting adjacent estuaries without incidence of xenoestrogenicity.

Genomic methods reveal independent demographic histories despite strong morphological conservatism in fish species

Human overexploitation of natural resources has placed conservation and management as one of the most pressing challenges in modern societies, especially in regards to highly vulnerable marine ecosystems. In this context, cryptic species are particularly challenging to conserve because they are hard to distinguish based on morphology alone, and thus it is often unclear how many species coexist in sympatry, what are their phylogenetic relationships and their demographic history. We answer these questions using morphologically similar species of the genus Mugil that are sympatric in the largest coastal Marine Protected Area in the Tropical Southwestern Atlantic marine province. Using a sub-representation of the genome, we show that individuals are assigned to five highly differentiated genetic clusters that are coincident with five mitochondrial lineages, but discordant with morphological information, supporting the existence of five species with conserved morphology in this region. A lack of admixed individuals is consistent with strong genetic isolation between sympatric species, but the most likely species tree suggests that in one case speciation has occurred in the presence of interspecific gene flow. Patterns of genetic diversity within species suggest that effective population sizes differ up to two-fold, probably reflecting differences in the magnitude of population expansions since species formation. Together, our results show that strong morphologic conservatism in marine environments can lead to species that are difficult to distinguish morphologically but that are characterized by an independent evolutionary history, and thus that deserve species-specific management strategies.

Ichthyofauna From Iranian Freshwater: Annotated Checklist, Diagnosis, Taxonomy, Distribution and Conservation Assessment

This is an annotated checklist of all the recognized and named taxa of freshwater fishes in Iran. It documents recent changes and controversies in the nomenclature and includes primary synonyms updated from the Jouladeh-Roudbar et al. (2015b) checklist. We provide an updated comprehensive listing of taxonomy, diagnostic and meristic characters, names, and conservation status, including detailed distribution maps. We strive to record the most recent justified taxonomic assignment in a hierarchical framework, providing annotations, including alternative possible arrangements, for some proposed changes. We provide common English and Persian names, and detail distributional data for all taxa, listing occurrence by basins, including indications of native, endemic, and translocated populations. We used the IUCN Red List Categories and Criteria for classifying species at high risk of global extinction. This checklist consists of 274 recognized species in 100 genera, 33 families, 20 orders and 3 classes. We also report and confirm for the first time the presence of seven species from Iran's basins: Aphanius kruppi, Capoeta kaput, Luciobarbus conocephalus, Oxynoemacheilus veyselorum, O. gyndes, O. hanae and Squalius latus. The confirmed freshwater fishes of Iran comprise 264 species in 97 genera, 33 families, 20 orders and 3 classes. The 241 endemic and native fish species can be divided into the following conservation statuses: 1 Extinct in the Wild (EW), 17 Critically Endangered (CR), 12 Endangered (EN), 15 Vulnerable (VU), 9 Near Threatened (NT), 148 Least Concern (LC) and 39 Data Deficient (DD). Forty-four fish species (18.3% of the 241 species listed) are officially regarded as globally Threatened (Critically Endangered [CR], Endangered [EN], or Vulnerable [VU]). These numbers and percentages of Threatened species have increased since the last checklist.

The complete mitochondrial genome of Moolgarda perusii (Teleostei: Mugilidae)

We determined the complete mitochondrial genome of Moolgarda perusii, which is 16,781 bp in length, and contains 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and a complete control region. The total base composition of the mitogenome is 28.7% T, 27.0% C, 28.5% A, and 15.9% G. Of the 13 PCGs, 11 PCGs start with an ATG codon. Eight PCGs use TAA/TAG/AGA as the termination codon, whereas five PCGs have incomplete stop codon TA/T. This study would be useful for further studying population genetics and understanding the phylogenetic relationship of the family Mugilidae.

Assembly rules of helminth parasite communities in grey mullets: combining components of diversity

Organisms aggregate in ecological communities. It has been widely debated whether these associations are explained by deterministic or, in contrast, random processes. The answer may vary, depending on the level of an organisational scale (α, β and γ) and the facet of diversity considered: taxonomic, functional and phylogenetic. Diversity at the level of a sampling unit (i.e. host individual) is the α diversity; β diversity represents the extent of dissimilarity in diversity among sampling units (within a level of an organisational scale, β1; between levels of an organisational scale, β2); and the total diversity of a system is γ diversity. Thus, the combination of facets and levels of a scale may be useful to disentangle the mechanisms driving the composition of a parasite community. Using helminth parasite taxonomic, functional, and a proxy for phylogenetic diversity of three species of grey mullets (Teleostei: Mugilidae) from the Mediterranean Sea, we show that random and deterministic processes of different nature explain the assemblage of parasite communities. The parasite community at a host individual (α) was invariably a random subset of the total diversity in the community for the three facets of diversity. At the β1 level, taxonomic diversity was lower than expected by chance, whereas functional diversity and the proxy for phylogenetic diversity were random. At the β2 level, diversity patterns suggested environmental filtering of the parasite assemblage: species, trait, and phylogenetic compositions of parasite communities seemed to depend primarily on the species of host, but also on the locality and season. Our study shows that parasite communities are not totally understood if any of the components (i.e. facets and levels) of diversity is neglected.

Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade

The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa. In this study, we used DNA-based approaches to investigate the evolutionary relationships, to explore the species diversity, and to elucidate the taxonomic status of sciaenid species/genera within the Indo-West Pacific clade. Three datasets were herein built for the above objectives: the combined dataset (248 samples from 45 currently recognized species) from one nuclear gene (RAG1) and one mitochondrial gene (COI); the dataset with only RAG1 gene sequences (245 samples from 44 currently recognized species); and the dataset with only COI gene sequences (308 samples from 51 currently recognized species). The latter was primarily used for our biodiversity exploration with two different species delimitation methods (Automatic Barcode Gap Discovery, ABGD and Generalized Mixed Yule Coalescent, GMYC). The results were further evaluated with help of four supplementary criteria for species delimitation (genetic similarity, monophyly inferred from individual gene and combined data trees, geographic distribution, and morphology). Our final results confirmed the validity of 32 currently recognized species and identified several potential new species waiting for formal descriptions. We also reexamined the taxonomic status of the genera, Larimichthys, Nibea, Protonibea and Megalonibea, and suggested a revision of Nibea and proposed a new genus Pseudolarimichthys.

Diversity and distribution of cryptic species within the Mugil cephalus species complex in Vietnam

Mugil cephalus sensu lato is a globally distributed complex of cryptic species whose distribution range and evolutionary history remains largely unknown. In the North West (NW) Pacific three species have been identified genetically among fish described morphologically as M. cephalus. Their distribution ranges are largely parapatric and has been proposed to mirror different thermal preferences. To date, few samples have been analyzed from South China Sea, which limits inferences on the evolutionary history of the species complex. We sampled fish identified morphologically as M. cephalus along Vietnamese shores and characterized them using the sequence polymorphism of two mitochondrial genes, the cytochrome oxidase I and cytochrome b. This demonstrated that all three species described in the NW Pacific are present in both northern and southern Vietnamese waters. Although the difference in species abundance reflects those observed in the NW Pacific, no phylogeographic pattern was revealed. In addition, no population structure was observed whatever the species or the distribution range considered, which indicates a significant level of gene flow that maintains genetic homogeneity of the three species. It is also conceivable that each species experienced a recent population expansion from a single ancestral population. Finally we suggest that if the cold waters of the NW Pacific present a physiologic challenge leading to the almost parapatric distribution of the three species, then it is likely that the warm surface temperatures of the South China Sea negate this barrier.

Multilocus resolution of Mugilidae phylogeny (Teleostei: Mugiliformes): Implications for the family's taxonomy

The interrelationships among mugilids (Mugiliformes: Mugilidae) remain highly debated. Using a mitochondrial gene-based phylogeny as criterion, a revised classification with 25 genera in the Mugilidae has recently been proposed. However, phylogenetic relationships of major mitochondrial lineages remain unresolved and to gain a general acceptance the classification requires confirmation based on multilocus evidence and diagnostic morphological characters. Here, we construct a species-tree using twelve nuclear and three mitochondrial loci and infer the evolution of 71 morphological characters. Our multilocus phylogeny does not agree with previous morphology-based hypotheses for the relationships within Mugilidae, confirms the revised classification with 25 genera and further resolves their phylogenetic relationships. Using the well-resolved multilocus phylogeny as the criterion, we reclassify Mugilidae genera into three new subfamilies (Myxinae, Rhinomugilinae, and Cheloninae) and one new, recombined, subfamily (Mugilinae). The Rhinomugilinae subfamily is further divided into four tribes. The revised classification of Mugilidae is supported by morpho-anatomical synapomorphies or a combination of characters. These characters are used to erect a key to the subfamilies and genera.

Next generation sequencing yields the complete mitochondrial genome of the largescale mullet, Liza macrolepis (Teleostei: Mugilidae)

In this study, the complete mitogenome sequence of largescale mullet (Teleostei: Mugilidae) has been sequenced by the next-generation sequencing method. The assembled mitogenome, consisting of 16,832 bp, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs genes, and a non-coding control region of D-loop. D-loop which has a length of 1094 bp is located between tRNA-Pro and tRNA-Phe. The overall base composition of largescale mullet is 27.8% for A, 30.1% for C, 16.2% for G, and 25.9% for T. The complete mitogenome may provide essential and important DNA molecular data for further phylogenetic and evolutionary analysis for Mugilidae.

Next generation sequencing yields the complete mitochondrial genome of the Hornlip mullet Plicomugil labiosus (Teleostei: Mugilidae)

In this study, the complete mitogenome sequence of hornlip mullet Plicomugil labiosus (Teleostei: Mugilidae) has been sequenced by next-generation sequencing method. The assembled mitogenome, consisting of 16,829 bp, had the typical vertebrate mitochondrial gene arrangement, including 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a non-coding control region of D-loop. D-loop contains 1057 bp length is located between tRNA-Pro and tRNA-Phe. The overall base composition of P. labiosus is 28.0% for A, 29.3% for C, 15.5% for G and 27.2% for T. The complete mitogenome may provide essential and important DNA molecular data for further population, phylogenetic and evolutionary analysis for Mugilidae.